You must show "reasonable cause" for the IRS to waive the penalty. An extension is timely filed if it is put in the mailbox on time, not when the IRS receives it. You need to write a letter to the IRS indicating that you filed the extension on time (if you did) and attach a proof of mailing if you have it. You should always file an extension by certified mail return receipt requested.
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Mr. Lively offers sound advice. Write a letter explaining that you did in fact file for the extension, that you have always filed timely and that you filed late but within the extension perioud. Finally, it is a good idea to file the extension electronically, then you are not at the mercy of the mail service.
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You have to show a "reasonable cause" in order for the IRS to waive the penalty. The important factor is when you mail the extension, not when the IRS receives it. You should write a letter to the IRS indicating that you filed the extension on time and attach a proof of mailing, such as a certified mail return receipt.